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Inland wetlands are highly diverse, productive ecosystems at the transition between terrestrial and aquatic environments, providing major services to society. They are also under high human pressure and have suffered a progressive decline in total area globally. Here, we describe the genetic diversity and demography of the endangered Lisbon arched-mouth nase Iberochondrostoma olisiponense occurring in the inland wetlands of a major river in southwestern Europe, within a context of extreme habitat changes. Our results highlight the presence of well-structured small population nuclei with evidence of sporadic gene flow at historical and contemporary time scales. Historical reconstructions suggest population isolation consistent with periods of unsuitable habitat conditions severing population connectivity, while small population sizes may be due to limited available habitat coupled to historical as well as recent restricted connectivity among river tributaries. Habitat contraction or loss due to decreased rainfall associated with climate change is expected to impact inland wetland fish regionally, raising additional conservation concerns on species with low genetic diversity and small effective population sizes as I. olisiponense . This study may serve as a proxy for taxa occurring in similar inland wetland ecosystems and may inform conservation efforts and planning regarding the expected drivers of population demographics, distribution and connectivity.

Climate change causes considerable shifts in the geographic distribution of species worldwide. Most data on range movements, however, derive from relatively short periods, within which it is difficult to distinguish directional shifts from random fluctuations. For detecting a shift, it is indispensable to delineate the range precisely. We propose a new method for the delineation based on percolation theory. We suggest marking the boundary between the connected and fragmented occurrence of the species (the hull). We demonstrate the advantages of this connectivity‐based method on simulated examples in which a metapopulation is advancing vs retreating along an environmental gradient with different velocities. The simulations show that the hull is a fractal and has the same dimension (7/4) even when the front is advancing or retreating relatively fast, compared to the generation time. It is particularly robust in the retreating (trailing) edge. Accordingly, we propose marking the range edge at the mean position of the hull, the 'connectivity limit' of the species. Theoretical considerations suggest that the position of the connectivity limit is statistically more reliable than those limits that are delineated according to the outermost occurrences, and the connectivity‐based method is broadly applicable to real‐life data.

The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota’s composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.

Aim: Conservationists have been using ecological niche modelling (ENM) to understand how climate change impacts species, estimate their extinction risk and assess species conservation status in the future. However, most ENMs are built using just current species occurrences. As short-term observations are naturally biased and incomplete in both geographical and climate spaces, palaeontologists have recommended the use of fossil data to improve species vulnerability assessments. Here, we used a time structured data set of the jaguar Panthera onca (Linnaeus, 1758) to test the implications of fossil data on distinct distribution dynamics and conservation status predicted by ENMs under future climate change scenarios. Location: The New World. Methods: We built two classes of ENMs, (i) using only current occurrences of P. onca and (ii) combining current and fossil information. Models were then projected onto current and future climates. Results: Niche models calibrated using fossil data broadly predicted more optimistic conservation statuses, with larger suitable areas for the species in the future, which are geographically nearest to its current distribution and better represented within protected areas (current network of protected areas will hold significant suitable areas). Main conclusions: Fossils provided complementary information about different climate conditions that species experienced though time and filled empty spaces in currently unoccupied fundamental niche. Our analyses reinforce the idea the fossil record is a valuable source of alternative information to increase the reliability of ENMs when assessing biodiversity risk. Combining ecological and palaeontological data for niche modelling increase our understanding about species responses to changing climates. Consequently, it potentially improves our knowledge on how to manage biodiversity by more reliably anticipating the effects of climate change and proactively—rather than reactively—planning conservation actions over longer periods going forward.

Aim To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black‐fronted tern (Chlidonias albostriatus), a specialist of the spatially and temporally dynamic environments of braided rivers. Location New Zealand. Methods We used a three‐pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b/control region) and phenotypic data (head‐bill length, bill depth, wing length, weight). We determined large‐scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding colonies and tested for isolation‐by‐distance between colonies. We investigated the level of fine‐scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding colonies to test for underlying mechanisms of population differentiation. Results Nuclear and mitochondrial DNA showed that across their range black‐fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation‐by‐distance. However, at fine geographical scales black‐fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions Significant fine‐scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonization of suitable habitat. For black‐fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.

The Tortonian–Messinian transition is associated with important climatic and oceanographic changes in the Mediterranean Basin, which have shaped both the biotic and abiotic nature of this setting. The morphological variability of the planktonic foraminifera Globorotalia menardii, a species that is highly sensitive to water column structure, has been investigated from the sedimentary archive of three Cretan sections across a west–east transect covering the Tortonian–Messinian Boundary. The present work explicitly focuses on test-size and coiling direction changes occurring during the 7.36–7.24 Ma time slice. On such a short timescale, the most important morphological differentiation accounts for the average size of G. menardii, which is mostly associated with evolutionary adaptation to new ecological niches during the latest Tortonian as a response to the environmental perturbations and ecological stress conditions preceding the Tortonian–Messinian Boundary. A combined thermal and/or salinity-driven stratification and thermocline development hypothesis has been suggested to explain the observed size variability. To ameliorate the accuracy of the proposed model and further determine which environmental parameter reflects the optimum conditions of the analysed species, additional sea surface temperature and salinity data derived from the same sampling intervals of the studied or additional Mediterranean sites are needed. The coiling direction of this species within the study time interval remained constant and not environmentally controlled.

Gymnosperms and angiosperms can co-occur within the same habitats but key plant traits are thought to give angiosperms an evolutionary competitive advantage in many ecological settings. We studied ontogenetic changes in competitive and facilitative interactions between a rare gymnosperm (Dioon sonorense, our target species) and different plant and abiotic neighbours (conspecific-cycads, heterospecific-angiosperms, or abiotic-rocks) from 2007 to 2010 in an arid environment of northwestern Mexico. We monitored survival and growth of seedlings, juveniles, and adults of the cycad Dioon sonorense to evaluate how cycad survival and relative height growth rate (RHGR) responded to intra- and interspecific competition, canopy openness, and nearest neighbour. We tested spatial associations among D. sonorense life stages and angiosperm species and measured ontogenetic shifts in cycad shade tolerance. Canopy openness decreased cycad survival while intraspecific competition decreased survival and RHGR during early ontogeny. Seedling survival was higher in association with rocks and heterospecific neighbours where intraspecific competition was lower. Shade tolerance decreased with cycad ontogeny reflecting the spatial association of advanced stages with more open canopies. Interspecific facilitation during early ontogeny of our target species may promote its persistence in spite of increasing interspecific competition in later stages. We provide empirical support to the long-standing assumption that marginal rocky habitats serve as refugia from angiosperm competition for slow-growing gymnosperms such as cycads. The lack of knowledge of plant–plant interactions in rare or endangered species may hinder developing efficient conservation strategies (e.g. managing for sustained canopy cover), especially under the ongoing land use and climatic changes.

Background Glaciations were recurrent throughout the Quaternary and potentially shaped species genetic structure worldwide by affecting population dynamics. Here, we implemented a multi-model inference approach to recover the distribution dynamics and demographic history of a Neotropical savanna tree, Tabebuia aurea (Bignoniaceae). Exploring different algorithms and paleoclimatic simulations, we used ecological niche modelling to generate alternative hypotheses of potential demographic changes through the last glacial cycle and estimated genetic parameters using coalescent modelling. Results Comparing predictions from demographic hypotheses with genetic parameters of modern populations, our findings revealed a likely scenario of population decline, with spatial displacement towards Northeast Brazil from the last glacial maximum to the mid-Holocene. Subsequently, populations expanded in response to the return of the climatically suitable conditions in Central-West Brazil. Nevertheless, a wide historical refugium across Central Brazil likely maintained large populations connected throughout time. The expected genetic signatures from such predicted distribution dynamics are also corroborated by spatial genetic structure observed in modern populations. Conclusion By exploring uncertainties inherent in multiple working hypotheses, we have shown that multi-model inference is a fruitful and efficient approach to recover the nature, timing and geographical context of the Tabebuia aurea population dynamic in response to the Quaternary climate changes.

Because of the dynamic nature of many managed habitats, proper evaluation of conservation efforts calls for models that take into account both spatial and temporal habitat dynamics. We develop a metapopulation model for successional-type systems, in which habitat quality changes over time in a predictable fashion. The occupancy and recruitment of the predatory saproxylic (dependent on dead wood) beetle Harminius undulatus was studied in a managed boreal forest landscape, covering 24449 ha, in central Sweden. In a first step, we analyzed the beetle's occupancy pattern in relation to stand characteristics, and the amounts of present and past habitat in the surrounding landscape. Managed forest is suitable habitat when ≥60 years old, and immediately after cutting, but not between the ages of 10 and 60 years. The observed occupancy of H. undulatus was positively correlated with the stand's age as habitat. We used a metapopulation model to predict the current probability of occurrence in each forest stand, given the spatiotemporal distribution of suitable forest stands during the last 50 years. Metapopulation parameters were estimated by matching predicted spatial distributions with observed spatial distributions. The model predicted observed spatial distributions better than a similar model that assumed constant habitat quality of each forest stand. Thus, metapopulation models for successional-type systems, such as dead wood dependent organisms in managed forest landscapes, should include habitat dynamics. An estimated 82% of the landscape-wide recruitment took place in managed stands, which covered 87% of the forest area, in comparison with 18% in unmanaged stands, which covered 13% of the forest area. Among the managed stand types, 2265;60-year-old stands and 3-7-year-old clear-cuttings contributed to 79% of the total recruitment while 8-59-year-old stands only contributed 3%. The results suggest the following guidelines to improve conditions for H. undulatus and other species with similar habitat requirements: (1) the proportion of the landscape constituted by younger stands should not be allowed to grow too large, (2) the rotation period of managed stands should not be allowed to be too short, and (3) dead wood should be retained and created at final cutting.

Regional persistence of species requires a positive balance between colonizations and local extinctions. In this study, we examined the amount of colonizations and extinctions and their likelihood as a function of patch size, isolation, and habitat characteristics of a riparian perennial plant, Erigeron acer subsp. decoloratus. We also studied the importance of patch dynamics to the regional population growth. Over five successive years, we counted the number of plant patches along 43 km of riverside. Most patches were small in area and population size. The annual finite growth rate in the number of patches varied between years, but the geometric mean was close to 1.0, indicating a viable patch network in spite of local extinctions. Extinction rate was highest on steep slopes and for small patches with few individual plants and a small patch area. When the patches were classified into different stage classes, the most common fate was stasis, i.e., the patch remained at the same stage. Patch survival and local, within-patch dynamics were most important during this five-year period. Between-patch dynamics (including colonization for example) accounted for 5-10% of annual transitions. The overall dynamics were relatively similar to those of other plant species subjected to riparian disturbance regimes. In the long run, the survival of the species depends on how well it is able to escape from competition from forest and meadow species and track the availability of suitable habitats. This kind of habitat tracking differs from classical metapopulation dynamics. In the former, local extinctions occur as a consequence of adverse changes in the habitat and recolonizations are rare, whereas metapopulation models assume a highly persistent habitat structure with frequent recolonizations. In this respect, the regional dynamics of perennial plants in disturbed riparian habitats may differ from classical metapopulations.